[Biopython-dev] User-defined annotations in Stockholm alignment file

[Peter Cock]

On Tue, Apr 5, 2016 at 8:58 AM, João Rodrigues
<j.p.g.l.m.rodrigues at gmail.com> wrote:
>> > My original question was why does AlignIO ignore "custom" annotations it
>> > doesn't know, while writing (StockholmIO, line 254)?
>>
>> https://github.com/biopython/biopython/blob/master/Bio/AlignIO/StockholmIO.py#L254
>>
>> Because as far as I know only a short list of accepted feature types for
>> the GS lines exist (from PFAM/RFAM). The associated comment about
>> this could have been prefixed with TODO - do you have a strong use
>> case for custom annotations?
>
> Not really, just a case where I want to add my own annotations to each
> sequence in an alignment. We could support "custom" annotations directly
> under the keys found in the Stockholm file, instead of trying to map them
> somewhere. That would keep the PFAM/RFAM keys "mappable" but extend the
> format if people want to add extra things. It's a shame such an
> annotation-friendly format can only take "official" annotations..

Its more I was strongly guided by PFAM as the only major user of the
annotations in the Stockholm format when I wrote the Biopython code.

Peter